#include <iostream>
#include <string>
#include <math.h>
#include <fstream>
#include <algorithm>
#include <stdio.h>
#include <boost/filesystem/path.hpp>
#include <boost/program_options.hpp>
#include "get_arg.h"



// link with -lboost_filesystem-gcc -lboost_program_options-gcc
// program_options_helper.cpp
//-lboost_filesystem-gcc-d
//-L/usr/local/lib





// my functions
#include <print_error.h>
#include <program_options_helper.h>
#include <stlhelper.h>
#define DEBUG_LEVEL 6
#include <debug_func.h>

using std::string;
using std::cerr;
using std::string;
using std::ofstream;
using std::ifstream;
using std::cerr;
using std::cout;
using std::max;
using boost::filesystem::path;
using namespace program_options_helper;
namespace po = boost::program_options_lg;

//_______________________________________________________________________________________

//		process_command_line_options

//				from command line
//				Created [9/13/2001]

//_______________________________________________________________________________________
bool process_command_line_options(int argc, char* argv[], t_program_args& args)
{

	//
	// checked mandatory arguments
	//
	po::options_description mandatory_args("Mandatory Arguments");
	mandatory_args.add_options()
	("input_file,i",		po::value<string>(&args.file_input)
										->set_name("FILE"),
									"File containing pairwise distances.");

	args.optional_args.add_options()
	("self_self,s",		po::bool_switch(&args.self_self),
							"Keep self-self comparisons.\n")
	("#comment,#",		po::value<string>(&args.comment_letters)
								->set_name("LETTERS")
								->default_value("#"),
							"Use one of these letters to begin a "
							"commented line.");


	args.use_results_summary();
	args.add_std_options();
	po::options_description all_args("");
	all_args.add(mandatory_args).add(args.optional_args);

	// parse command line
	po::variables_map vm;
	po::store(po::command_line_parser(argc, argv).options(all_args).run(), vm);
	po::notify(vm);

	if (vm.count("version"))
	{
		print_version(cerr, *argv, "1.0\n"
			"\tHistory: \n\n"
			"\tv 1.0"
			"17-07-2005\1"
			"First Version\1"
			"Uses crc hashes. Which is why STDIN is not used.\n"
			);
		return false;
	}
	if (vm.count("help"))
	{
		string exe_description =
					"Takes file of identifier pairs and distances and prints out the pairs "
					"with the lowest distances in case of duplicates.\n";

		po::options_description visible_args("");
		visible_args.add(mandatory_args).add(args.optional_args);
		print_usage(cerr, string(*argv), "--input_file FILE [OPTIONS]\n"
											" > UNIQUE.RESULTS",
							visible_args, exe_description, 80);
		return false;
	}
	check_required_options(vm, mandatory_args);


	args.open_err_log();
	return true;
}













